Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

add cram index #427

Merged
merged 5 commits into from
Nov 2, 2023
Merged

add cram index #427

merged 5 commits into from
Nov 2, 2023

Conversation

rannick
Copy link
Collaborator

@rannick rannick commented Oct 30, 2023 •
edited
Loading

Closes #423

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@rannick rannick self-assigned this Oct 30, 2023
@github-actions
Copy link

github-actions bot commented Oct 30, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0b67a98

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-01 11:11:34

fevac
fevac approved these changes Nov 1, 2023
View reviewed changes
Copy link
Contributor

@fevac fevac left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Awesome! Make sure it runs successfully with the test case before merging 🚀

@rannick
Copy link
Collaborator Author

rannick commented Nov 2, 2023

It does (the cram part, megafusion fails atm, to be fixed in the vcf_collect pr)

@rannick rannick merged commit cc52314 into dev Nov 2, 2023
6 checks passed
@rannick rannick deleted the cram_index branch November 8, 2023 12:23
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@fevac fevac fevac approved these changes

Assignees

@rannick rannick

Labels
waiting-for-review
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Add cram index to same directories as cram files
2 participants
@rannick @fevac